OEDesignUnit

Attention

This API is currently available in C++ and Python.

class OEDesignUnit : public OESystem::OEBase

This is a container class derived from OEBase that holds all molecules needed to construct a model-ready biomolecular system.

Constructors

OEDesignUnit()

Default constructor.

Molecule constructors

Note

Molecule constructors are intended for already prepared molecules. They requires a target structure, as well as either a ligand or a list of binding site residues. Solvent and co-factors are optional, and are only set if the molecules passed are valid. The target molecule is not split into components and no structure preparation take place. A title will be generated based on the names of the provided molecules, but can be set manually afterwards.

OEDesignUnit(const OEChem::OEMolBase& target, const OEChem::OEMolBase& ligand, const OEChem::OEMolBase& solvent=OEChem::OEGraphMol(), const OEChem::OEMolBase& cofactors=OEChem::OEGraphMol(), const unsigned targetID=OEDesignUnitComponents::Protein)

Target-ligand constructor

OEDesignUnit(const OEChem::OEMolBase& target, const std::vector<std::string>& siteResidues, const OEChem::OEMolBase& solvent=OEChem::OEGraphMol(), const OEChem::OEMolBase& cofactors=OEChem::OEGraphMol(), const unsigned targetID=OEDesignUnitComponents::Protein);

Apo target constructor

operator=

operator bool

Clear

CreateCopy

CreateCopy(OEDesignUnit self)

Deep copy constructor that returns a copy of the object. The memory for the returned OEDesignUnit object is dynamically allocated and owned by the caller.

GetComponent

GetComponent(OEDesignUnit self, OEMolBase molecule, componentID)

Returns a const reference to the molecule on the OEDesignUnit that is associated with the input componentID. Note that this function only works for single molecule components (e.g. protein, ligand, etc). This function requires an empty OEMolBase or it will clear the incoming molecule.

GetComponentID

GetComponentID(OEDesignUnit self, componentTag)

Returns the internal unsigned integer representation of the componentTag string from the OEDesignUnit object.

GetComponentTag

GetComponentTag(OEDesignUnit self, componentID)

Returns the string tag representation of the componentID unsigned integer from the OEDesignUnit object.

GetComponents

GetComponents(self, *args)
GetComponents(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, bool bondCovalent=True)
GetComponents(OEDesignUnit self, OEMolBase mol, unsigned int componentMask)
GetComponents(OEDesignUnit self, OEMolBase mol)

The function creates a single output mol from the components given in the componentMask bit mask. The bit mask can be constructed using unsigned integers stored in the OEDesignUnitComponents namespace. The function returns a boolean value to alert if the operation was successful. Note that this function only works for a list of components (e.g. other_ligands, excipients, etc). The optional predicate can be used to subset some of the components in the specified bit mask. The predicate does not have to be complete, e.g. two water molecules can be specified to subset the solvent category, but that will not subset the protein component also included in that mask. In essence the predicate is checked to see if it matches part of a design unit component and only in this case does it take effect.

GetComponentsWithin

GetComponentsWithin(self, *args)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, unsigned int withinMask, double dist=5.0, bool includeSelf=False, bool bondCovalent=True)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, unsigned int withinMask, double dist=5.0, bool includeSelf=False)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, unsigned int withinMask, double dist=5.0)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask, unsigned int withinMask)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol, unsigned int componentMask)
GetComponentsWithin(OEDesignUnit self, OEMolBase mol)

The function creates a single output mol from the components given in the componentMask bit mask that fall within a dist distance of components given in the withinMask bit mask. All bit masks can be constructed using unsigned integers stored in the OEDesignUnitComponents namespace. If the boolean bondCovalent flag is set, all components that should be covalently bonded will have bonded added in the output mol. The function returns a boolean value to alert if the operation was successful.

GetDataType

GetDataType(OEDesignUnit self)

This pure virtual function is used to perform run-time type identification. The value returned by the method should be equivalent to the value returned by OEGetDataType using the OEDesignUnit derived class type as the template argument.

GetIDs

GetIDs(OEDesignUnit self)

Returns a vector of the component IDs stored on the OEDesignUnit object.

GetLigand

GetLigand(OEDesignUnit self, OEMolBase molecule)

Returns success based on a valid copy of the ligand molecule in the OEDesignUnit object.

    lig = oechem.OEGraphMol()
    if not du.GetLigand(lig):
        oechem.OEThrow.Fatal("Error: Could not extract ligand from the OEDesignUnit.")
    oechem.OEWriteMolecule(ofs, lig)

Whole example script can be downloaded from here.

GetMetal

GetMetal(OEDesignUnit self, OEMolBase molecule)

Returns success based on a valid copy of the metal in the OEDesignUnit object.

GetNucleicAcid

GetNucleicAcid(OEDesignUnit self, OEMolBase molecule)

Returns success based on a valid copy of the nucleic acid molecule in the OEDesignUnit object.

GetPDBMetaData

GetPDBMetaData(OEDesignUnit self, OEMolBase mol)

Returns success based on a valid copy of the PDB metadata in the OEDesignUnit object.

See also

• OEResidueToString function.

GetPackingResidues

GetPackingResidues(OEDesignUnit self, OEMolBase molecule)

Returns success based on a valid copy of the packing residue molecule in the OEDesignUnit object.

GetProtein

GetProtein(OEDesignUnit self, OEMolBase molecule)

Returns success based on a valid copy of the protein molecule in the OEDesignUnit object. Note that this function requires an empty OEMolBase or it will clear the incoming molecule.

GetReceptor

GetReceptor(self, *args)

GetReceptor(OEDesignUnit self, OEReceptor receptor)

Returns a reference to the receptor on the OEDesignUnit object.

GetReceptor(OEDesignUnit self)

Returns success based on a valid copy of the receptor in the OEDesignUnit object.

GetSiteResidues

GetSiteResidues(OEDesignUnit self)

Returns a vector of the site residue strings stored on the OEDesignUnit object. This function calls the OEResidueToString function with “:” delimiter.

GetSolvent

GetSolvent(OEDesignUnit self, OEMolBase molecule)

Returns success based on a valid copy of the solvent molecule in the OEDesignUnit object.

GetStructureQuality

GetStructureQuality(OEDesignUnit self)

Returns the OEStructureQuality class stored on the OEDesignUnit object.

See also

• OEStructureQuality class

GetTransform

GetTransform(OEDesignUnit self, OETrans trans)

Returns success based on a valid copy of the input OETrans object in the OEDesignUnit object.

See also

• OETrans class

GetTaggedComponents

GetTaggedComponents(self, *args)
GetTaggedComponents(OEDesignUnit self, unsigned int componentMask)
GetTaggedComponents(OEDesignUnit self)

Returns an OEIter of all molecules and corresponding molecular tags stored on the OEDesignUnit object. A bit mask of desired components can be constructed from constants in the OEDesignUnitComponents namespace and be passed in via the componentMask argument.

GetTags

GetTags(OEDesignUnit self)

Returns a vector of the tags of the molecules stored on the OEDesignUnit object.

GetTarget

GetTarget(OEDesignUnit self, OEMolBase molecule)

Returns success based on a valid copy of the target molecule in the OEDesignUnit object.

GetTargetComponentID

GetTargetComponentID(OEDesignUnit self)

Returns the component ID from the OEDesignUnitComponents namespace of the target molecule on the OEDesignUnit object.

GetTargetComponentTag

GetTargetComponentTag(OEDesignUnit self)

Returns the string tag of the title of the OEDesignUnit object.

GetTitle

GetTitle(OEDesignUnit self)

Returns the title of the OEDesignUnit object.

GetAltLoc

GetAltLoc(OEDesignUnit self)

Returns the alternate location code used to generate the OEDesignUnit.

HasAltLoc

HasComponent

HasComponent(OEDesignUnit self, unsigned int componentID)

Checks that a molecule given by the componentID from the OEDesignUnitComponents namespace has been set on the OEDesignUnit object.

HasLigand

HasLigand(OEDesignUnit self)

Checks that the ligand molecule of the OEDesignUnit object has been set.

HasMetal

HasMetal(OEDesignUnit self)

Checks that the metal molecule of the OEDesignUnit object has been set.

HasNucleicAcid

HasNucleicAcid(OEDesignUnit self)

Checks that the nucleic acid molecule of the OEDesignUnit object has been set.

HasPDBMetaData

HasPDBMetaData(OEDesignUnit self)

Checks that the PDB metadata of the OEDesignUnit object has been set.

HasPackingResidues

HasPackingResidues(OEDesignUnit self)

Checks that the packing residue molecule of the OEDesignUnit object has been set.

HasProtein

HasProtein(OEDesignUnit self)

Checks that the protein molecule of the OEDesignUnit object has been set.

HasReceptor

HasReceptor(OEDesignUnit self)

Checks that the OEDesignUnit object contains a valid receptor.

HasSiteResidues

HasSiteResidues(OEDesignUnit self)

Checks that the site residues of the OEDesignUnit object has been set.

HasSolvent

HasSolvent(OEDesignUnit self)

Checks that the solvent molecule of the OEDesignUnit object has been set.

HasStructureQuality

HasStructureQuality(OEDesignUnit self)

Checks that the internal OEStructureQuality object stored on the OEDesignUnit has been set.

HasTransform

HasTransform(OEDesignUnit self)

Checks that the internal OETrans object stored on the OEDesignUnit has been set.

HasTarget

HasTitle

IsDataType

IsDataType(OEDesignUnit self, void const * arg2)

Returns whether the type is the same as the instance this method is called on.

SetTitle

SetTitle(OEDesignUnit self, title)

Sets the title of the OEDesignUnit object.

ClearReceptor

ClearReceptor(OEDesignUnit self)

Clears the stored OEReceptor object.

ClearComponent

bool ClearComponent(OEDesignUnit self, const std::string& componentTag, int listIndex = -1)
bool ClearComponent(OEDesignUnit self, unsigned componentID, int listIndex = -1)

Clears a specified component. The listIndex is intended for listComponents, e.g. co-factors. If the listIndex is -1 the entire list is removed, otherwise only the co-factor with the given index is removed.